Have apply_patch.py/checkout.py stage git patches instead of committing them

tests/checkout_test.py

 #!/usr/bin/env python
 # Copyright (c) 2012 The Chromium Authors. All rights reserved.
 # Use of this source code is governed by a BSD-style license that can be
 # found in the LICENSE file.
 
 """Unit tests for checkout.py."""
 
 import logging
 import os
 import shutil
@@ skipping 405 matching lines @@
       expected = self._log()
 
     actual = self._log(log_from_local_repo=True)
     self.assertEquals(expected, actual)
 
   def get_trunk(self, modified):
     tree = {}
     for k, v in self.FAKE_REPOS.git_hashes[
         self.FAKE_REPOS.TEST_GIT_REPO][1][1].iteritems():
       assert k not in tree
-      tree[k] = v 
+      tree[k] = v
 
     if modified:
       content_lines = tree['chrome/file.cc'].splitlines(True)
       tree['chrome/file.cc'] = ''.join(
           content_lines[0:5] + ['FOO!\n'] + content_lines[5:])
       tree['bin_file'] = '\x00'
       del tree['extra']
       tree['new_dir/subdir/new_file'] = 'A new file\nshould exist.\n'
     return tree
 
@@ skipping 26 matching lines @@
   def testProcess(self):
     self._test_process(self._get_co)
 
   def _testPrepare(self):
     self._test_prepare(self._get_co(None))
 
   def testMove(self):
     co = self._get_co(None)
     self._check_move(co)
     out = subprocess2.check_output(
-        ['git', 'diff', 'HEAD~', '--name-status'], cwd=co.project_path)
+        ['git', 'diff', '--staged', '--name-status'], cwd=co.project_path)
     out = sorted(out.splitlines())
     expected = sorted(
       [
         'A\tchromeos/views/webui_menu_widget.h',
         'D\tchromeos/views/DOMui_menu_widget.h',
       ])
     self.assertEquals(expected, out)
 
 
 class SvnCheckout(SvnBaseTest):
@@ skipping 244 matching lines @@
   if '-v' in sys.argv:
     DEBUGGING = True
     logging.basicConfig(
         level=logging.DEBUG,
         format='%(levelname)5s %(filename)15s(%(lineno)3d): %(message)s')
   else:
     logging.basicConfig(
         level=logging.ERROR,
         format='%(levelname)5s %(filename)15s(%(lineno)3d): %(message)s')
   unittest.main()